python-neo/.github/workflows/io-test.yml at master · b-grimaud/python-neo · GitHub

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name: NeoIoTest

on:
  workflow_call:
    inputs:
      os:
        required: true
        type: string

concurrency:  # Cancel previous workflows on the same pull request
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  build-and-test:
    name: Test on (${{ inputs.os }}) (${{ matrix.python-version}}) (${{ matrix.numpy-version }})
    runs-on: ${{ inputs.os }}
    strategy:
      fail-fast: true
      matrix:
        python-version: ['3.10', '3.14']
        numpy-version: ['1.26', '2.3.3']
        exclude:
           - python-version: '3.10'
             numpy-version: '2.3.3'
           - python-version: '3.14'
             numpy-version: '1.26'
    defaults:
      # by default run in bash mode (required for conda usage)
      run:
        shell: bash -l {0}
    steps:

      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Get current year-month
        id: date
        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

      - name: Get ephy_testing_data current head hash
        # the key depend on the last commit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git
        id: ephy_testing_data
        run: |
          echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT

      - uses: actions/cache/restore@v4
        # Loading cache of ephys_testing_dataset
        id: cache-datasets
        with:
          path: ~/ephy_testing_data
          key: ${{ runner.os }}-datasets-${{ steps.ephy_testing_data.outputs.dataset_hash }}
          restore-keys: ${{ runner.os }}-datasets-

      - uses: conda-incubator/setup-miniconda@v3
        with:
          activate-environment: neo-test-env-${{ matrix.python-version }}
          python-version: "${{ matrix.python-version }}"

      # TEST NOT USING CACHE
      #- name: Get current dependencies hash
      #  id: dependencies
      #  run: |
      #    echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT

      #- uses: actions/cache/restore@v3
        # the cache for python package is reset:
        #   * every month
        #   * when package dependencies change
      #  id: cache-conda-env
      #  with:
      #    path: /usr/share/miniconda/envs/neo-test-env-${{ matrix.python-version }}
      #    key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
          # restore-keys match any key that starts with the restore-key
       #   restore-keys: |
       #     ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-
       #     ${{ runner.os }}-conda-env-

      - name: Install testing dependencies
        # testing environment is only created from yml if no cache was found
        # restore-key hits should result in `cache-hit` == 'false'
        #if: steps.cache-conda-env.outputs.cache-hit != 'true'
        run: |
          conda install pip numpy=${{ matrix.numpy-version }} -c conda-forge
        # this command is for updating cache. We are resting removal.
        # conda env update --name neo-test-env-${{ matrix.python-version }} --file environment_testing.yml --prune

      - name: Install git-annex
        # this is the trick from the spikeinterface repo for getting git-annex to work with datalad
        # see https://github.com/SpikeInterface/spikeinterface/pull/3877 for more info
        shell: bash
        run: |
          pip install datalad-installer
          datalad-installer --sudo ok git-annex --method datalad/packages
          git config --global filter.annex.process "git-annex filter-process"  # recommended for efficiency

      - name: Configure git
        run: |
          git config --global user.email "neo_ci@fake_mail.com"
          git config --global user.name "neo CI"

      - name: Python version
        run: |
          which python
          python --version

      - name: Install neo including dependencies
        # installation with dependencies is only required if no cache was found
        # restore-key hits should result in `cache-hit` == 'false'
        # if: steps.cache-conda-env.outputs.cache-hit != 'true'
        run: |
          pip install --upgrade -e .
          pip install .[test]

      # TEST NOT USING CACHE
      #- name: Install neo without dependencies
        # only installing neo version to test as dependencies should be in cached conda env already
      #  if: steps.cache-conda-env.outputs.cache-hit == 'true'
      #  run: |
      #    pip install --no-dependencies -e .

      - name: Pip list
        run: |
          pip list

      - name: Conda list
        run: |
          conda list

      - name: Test with pytest
        env:
          HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_local_plugin_path
        run: |
          # only neo.rawio and neo.io
          pytest --cov=neo neo/test/rawiotest
          pytest --cov=neo neo/test/iotest